How to make TE gtf file from gff3 for TEtranscripts reference?

Question

[maureenwidyawan]

Hi I'm new to bioinformatics. So I'm analyzing transposable elements (TE) in RNA-seq of Musa acuminata (banana) and I'm planning on using TEtranscripts. TEtranscripts needs references (genome and TE) in gtf format. I can't find banana database that's in gtf format but I found the genome and TE references from Banana Genome Hub in gff3 format.

This is what the TE gtf file looks like

 ##gff-version 3
##sequence-region chr01 1 29070452
chr01   RepeatExplorer  repeat_region   10954   11572   .   +   .   Name=Ma_chr01-te0111212;Note=LTR~ Gypsy~ Chromovirus~ Monkey;_Label=LTR-Gypsy-Chromovirus-Monkey;ID=Ma_chr01-te0111212
chr01   RepeatExplorer  repeat_region   30672   30962   .   +   .   Name=Ma_chr01-te0111213;Note=LTR~ Copia~ SireMaximus;_Label=LTR-Copia-SireMaximus;ID=Ma_chr01-te0111213
###
chr01   RepeatExplorer  repeat_region   31004   31490   .   +   .   Name=Ma_chr01-te0111214;Note=LTR~ Copia~ SireMaximus;_Label=LTR-Copia-SireMaximus;ID=Ma_chr01-te0111214
chr01   RepeatExplorer  repeat_region   31594   31924   .   +   .   Name=Ma_chr01-te0111215;Note=LTR~ Copia~ SireMaximus;_Label=LTR-Copia-SireMaximus;ID=Ma_chr01-te0111215

I wonder if there are any tools that can help me convert gff to gtf format? (I tried gffread but didn't work). And also as the TE gff files are available per chromosome, how can I merge those files?

Thank you for sparing your time helping me :)

[h.mon]

The TEtranscripts site where you can find the annotated TE gtfs includes a script (makeTEgtf.pl) to create gtfs from various sources, for example, from RepeatMasker files downloaded from USCS.

[maureenwidyawan]

Thank you! Do you happen to know how to merge gff files? Because I have 11 TE gff files (one for each chromosome). I think I need to merge them if I want to use them.

Answer 1

[Juke34]

You can try AGAT It should work.

[maureenwidyawan]

Thanks! I'll try it :)